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Table 2 Correlations between the estimated TF-binding affinities based on inferred PBEM from in vitro data and the measured TF tag counts from in vivo ChIP-seq experiment

From: Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence

ChIP-Seq Called peaks Rank Paired PBMs agreement R (top 500) R (top 1000) R (top 2000) R (all peaks)
TF_31 (Zfx) 10338 8 Good 0.38978 0.35943 0.33566 0.25502
TF_44 (Gata4) 16979 22 Good 0.29675 0.28458 0.2645 0.15614
TF_23 (Tbx20) 4012 33 Good 0.077781 0.062428 0.043291 0.043338
TF_25 (Tbx5) 56352 41 Bad 0.062865 0.090766 0.073079 0.053016
TF_40 (Esrrb) 21647 59 Bad 0.16334 0.12283 0.10351 0.064026
  1. In the table, the first column describes ID of mouse TFs in DREAM5 challenges and the TF names to the ChIP-seq experiments; Called peaks are the number of called peaks in the ChIP-seq data; Rank represents rank order of TFs that were sorted in decreasing order of the final performance score across all tested algorithms in Figure 2 of original publication [1]; paired PBMs agreement indicates the agreement between training and testing PBMs; R is square root of R-square statistic from a linear regression model, where the relationship between the predicted TF-binding affinities and the observed ChIP-seq tag counts is investigated.